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- PDB-3u6r: Three dimensional structure of broadly neutralizing anti - Hepati... -

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Basic information

Entry
Database: PDB / ID: 3u6r
TitleThree dimensional structure of broadly neutralizing anti - Hepatitis C virus (HCV) glycoprotein E2 single chain FV fragment 1:7
Components
  • Antibody 1:7 (Heavy chain)
  • Antibody 1:7 (Light chain)
KeywordsIMMUNE SYSTEM / Ig-like domain / neutralizing single chain FV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsGilmartin, A.A. / Lamp, B. / Ruemenapf, T. / Persson, A.A. / Rey, F.A. / Krey, T.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: High-level secretion of recombinant monomeric murine and human single-chain Fv antibodies from Drosophila S2 cells.
Authors: Gilmartin, A.A. / Lamp, B. / Rumenapf, T. / Persson, M.A. / Rey, F.A. / Krey, T.
History
DepositionOct 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 1:7 (Heavy chain)
L: Antibody 1:7 (Light chain)
A: Antibody 1:7 (Heavy chain)
B: Antibody 1:7 (Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9945
Polymers61,8984
Non-polymers961
Water1,04558
1
H: Antibody 1:7 (Heavy chain)
L: Antibody 1:7 (Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0453
Polymers30,9492
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-27 kcal/mol
Surface area10690 Å2
MethodPISA
2
A: Antibody 1:7 (Heavy chain)
B: Antibody 1:7 (Light chain)


Theoretical massNumber of molelcules
Total (without water)30,9492
Polymers30,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.485, 105.744, 105.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Antibody 1:7 (Heavy chain)


Mass: 15723.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT-scFv-Strep / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody Antibody 1:7 (Light chain)


Mass: 15225.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT-scFv-Strep / Production host: Drosophila melanogaster (fruit fly)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.54M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.67→37.36 Å / Num. all: 17118 / Num. obs: 15834 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 58.77 Å2
Reflection shellResolution: 2.67→2.81 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1316 / % possible all: 54.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKU

3fku


Resolution: 2.67→24.57 Å / Cor.coef. Fo:Fc: 0.9265 / Cor.coef. Fo:Fc free: 0.8905 / SU R Cruickshank DPI: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Maximum Likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 990 6.27 %RANDOM
Rwork0.1902 ---
all0.1967 17077 --
obs0.1929 15793 92.48 %-
Displacement parametersBiso mean: 50.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.4315 Å20 Å20 Å2
2---1.3103 Å20 Å2
3---7.7417 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 2.67→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 5 58 3667
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013698HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195030HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1230SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes539HARMONIC5
X-RAY DIFFRACTIONt_it3698HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion20.23
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4202SEMIHARMONIC4
LS refinement shellResolution: 2.67→2.85 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2604 108 5.91 %
Rwork0.2382 1719 -
all0.2396 1827 -
obs-1827 92.48 %

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